Why do I get a weird copy number in the tumour?

Question

[w.jaratlerdsiri]

Please see the attached. I try to understand why Tumour 1 has most of the copy number equal to 1, but most of my past analyses (e.g. sequenza) and other works have most in the copy number =2 (same as Normal). Could you give me an insight of this interpretation?

I ran: 1.cnvkit.py batch 2.cnvkit.py export theta Sample_Tumor.cns Sample_Normal.cnr -o Sample.theta2.input 3./path/to/theta2/bin/RunTHetA Sample.theta2.input

Note I ran THeTA2 to get tumour purity and number of subclones. Is it something due to that "CNVkit only reports the estimated log2 copy ratio, and does not currently attempt a formal statistical test for estimating integer copy number"?

Thankyou, James

Answer 1

[Eric T.]

The procedure you ran is correct. THetA2 is not perfect, and it particularly struggles with samples that are noisy or have few large-scale CNVs. In this case I'd probably trust the result you got from Sequenza over THetA2.

I've updated CNVkit's "export theta" command to make it easy to run THetA2 with SNP allele frequencies to improve the results; you can try the latest CNVkit and THetA2 code from GitHub and see if that helps.

Otherwise, users have reported getting good results from PyClone, and it should be possible to run BubbleTree with CNVkit's segments if you coerce the data into the right form. Or you can proceed with Sequenza's purity estimate -- you only need a rough estimate of tumor purity to get useful results from CNVkit's call command.

[Ming Tommy Tang]

Hi Eric, may I ask how does the call command work? I have segment file output from sequenza. sequenza also gives a purity estimate. I want to scale the segment depth ratio by the tumor purity. The output of sequenaza segments is diff from cnvkit, so I am not sure how to use the call command. Thanks!

Answer 2

[hywg]

How do you run cnvkit.py call on DNAnexus platform? I can run it on the Linux commandline, but found no way to run it on DNAnexus. Thanks in advance.

[Eric T.]

The DNAnexus app doesn't expose all of CNVkit's functionality, only the basic pipeline. To run the call command you'll need to install CNVkit on your own Linux or OS X machine.